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The bigger flaw is that James was talking about pitchers who were extreme GB pitchers, not the top 25% but the top 2-3%. Pitchers whose gb rates differed from the median by a much more statistically significant amount. And not coincidentally were extremely effective.

No flaw in comparing different sized groups, as long as you recognize they'll have different levels of variation.

The article looks at the top 10%, T(AHB). Now, maybe you want to argue that it has to be on the top 2-3%, but at that point you are getting down to numbers where it would be close to impossible to prove much of anything.